Variant report

Variant	rs3213542
Chromosome Location	chr6:100966006-100966007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:100963737..100966583-chr6:100995209..100997563,2	MCF-7	breast:
2	chr6:100960099..100962319-chr6:100964454..100967453,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12661493	0.97[ASN][1000 genomes]
rs12662153	0.97[ASN][1000 genomes]
rs12663913	0.94[ASN][1000 genomes]
rs1501356	0.97[ASN][1000 genomes]
rs17060762	0.91[ASN][1000 genomes]
rs171257	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2398133	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs240165	0.87[EUR][1000 genomes]
rs240166	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs240768	0.80[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs240777	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs240779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240782	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs240785	0.82[ASW][hapmap];0.80[CEU][hapmap];0.82[LWK][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs33988845	0.97[EUR][1000 genomes]
rs401864	0.89[GIH][hapmap]
rs6931919	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72939355	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs72949504	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv886444	chr6:100961198-101084946	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3213542	GRIK2	cis	Artery Tibial	GTEx
rs3213542	CCNC	cis	lymphoblastoid	seeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100949800-100966400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:100951600-100969800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:100952600-100967600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:100952800-100997400	Weak transcription	A549	lung
5	chr6:100953000-100968400	Weak transcription	Fetal Kidney	kidney
6	chr6:100953200-100966200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:100953400-100966600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:100953400-100967400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:100954200-100966200	Strong transcription	Dnd41	blood
10	chr6:100954600-100986200	Weak transcription	Spleen	Spleen
11	chr6:100954800-100966200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:100955200-100972800	Weak transcription	Right Ventricle	heart
13	chr6:100955800-100966400	Weak transcription	Colonic Mucosa	Colon
14	chr6:100955800-100966800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:100955800-100991200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:100956800-100966200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr6:100957400-100992400	Weak transcription	Small Intestine	intestine
18	chr6:100958200-100976600	Weak transcription	NHDF-Ad	bronchial
19	chr6:100958600-100974000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:100959800-100966800	Weak transcription	Fetal Stomach	stomach
21	chr6:100960200-100966200	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:100960200-100978000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:100960600-100967400	Weak transcription	Fetal Thymus	thymus
24	chr6:100960600-100973800	Weak transcription	HUVEC	blood vessel
25	chr6:100960600-100990200	Weak transcription	Brain Substantia Nigra	brain
26	chr6:100960800-100966200	Weak transcription	Liver	Liver
27	chr6:100960800-100966400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:100960800-100966600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:100960800-100966800	Weak transcription	Fetal Lung	lung
30	chr6:100960800-100966800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:100960800-100967000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:100960800-100967000	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:100960800-100969400	Weak transcription	Esophagus	oesophagus
34	chr6:100960800-100970800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:100960800-100971200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:100960800-100971200	Weak transcription	Thymus	Thymus
37	chr6:100960800-100974000	Weak transcription	NH-A	brain
38	chr6:100960800-100977600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:100960800-100981000	Weak transcription	Gastric	stomach
40	chr6:100960800-100986000	Weak transcription	GM12878-XiMat	blood
41	chr6:100960800-100986200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:100960800-100986600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:100960800-100989600	Weak transcription	K562	blood
44	chr6:100960800-100989800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:100960800-101035000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:100961000-100986600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr6:100961000-100987200	Weak transcription	Osteobl	bone
48	chr6:100961000-100988800	Weak transcription	NHEK	skin
49	chr6:100961000-100991200	Weak transcription	HSMMtube	muscle
50	chr6:100961000-100992000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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